Thesis (MSc (Genetics))--University of Stellenbosch, 2010. / Thesis presented in partial fulfilment of the requirements for the degree of Master of Science (MSc) in Genetics at Stellenbosch University. / ENGLISH ABSTRACT: The prevalence of adverse drug reactions (ADR) and treatment failure in South Africa requires urgent addressing and it is the aim of pharmacogenetics to aid in the alleviation of these ADRs and treatment failures. However, considering the high level of genetic diversity present in African populations, preliminary analysis of the genetic profiles of South African populations is required before pharmacogenetics can be successfully implemented in the South African context. Therefore this study aimed to characterise the gene encoding the drug metabolising enzyme, CYP2C19, in the South African Xhosa population. To identify the common CYP2C19 sequence variation present in the Xhosa population, semiautomated sequence analysis of CYP2C19 was performed on 15 healthy Xhosa individuals. The variation detected was then prioritised through various in silico analyses for further restriction fragment length polymorphism (RFLP) genotyping in an additional 85 healthy Xhosa individuals to confirm the frequencies of the prioritised variants in a larger cohort, while the copy number variation (CNV) present in the entire 100 Xhosa individuals was analysed with the use of duplex real-time PCR. To functionally validate the in silico data obtained for the 5’-upstream variants, dual luciferase reporter assays were utilised. In addition to these analyses, multi-species comparisons were used to highlight regions of high sequence similarity within the 5’-upstream regions, while CpG island analysis was utilised to identify possible CpG islands occurring within and around the CYP2C genes. Sequence analysis of the CYP2C19 gene revealed 30 variants, of which five were novel. Subsequent to RFLP analysis, the frequencies of the allele-defining variants detected in this population, namely CYP2C19*2, CYP2C19*9, CYP2C19*15 and CYP2C19*17 were found to be 0.21, 0.09, 0.09 and 0.10, respectively. Additionally, the novel non-synonymous V374I variant, which was designated CYP2C19*28, was found to occur at a frequency of 0.01. Dual luciferase reporter assays revealed that the construct containing the rs7902257 variant, demonstrated a significant decrease in the fold induction observed when compared to the “wild type” construct (P = 0.0077). This variant was designated CYP2C19*27 and was detected at a frequency of 0.33 in the Xhosa population. In addition to this, multi-species comparisons revealed four highly conserved regions, all of which were present within LINE L1 repetitive elements. Although putative CpG islands were identified in and around the CYP2C genes, no direct correlations could be made between the differences in expression observed between the genes and the presence of the CpG islands. The role of these islands with regards to the epigenetic regulation of these genes therefore remains to be elucidated. To our knowledge, this study provides the most comprehensive data for CYP2C19 in a South African population and shows that the Xhosa population displays a unique genetic profile, which differs from those of other populations, including the Cape Mixed Ancestry population of South Africa. Thus, novel genotyping platforms need to be developed in order to successfully apply pharmacogenetics to the diverse populations residing in South Africa. / AFRIKAANSE OPSOMMING: Die doel van Farmakogenetika is om daadwerklike aandag aan die hoë voorkoms van nadelige geneesmiddel reaksies en mislukte behandelings te skenk en om hierdie voorkoms in Suid-Afrika te verlaag. Die bevolkingsgroepe van Afrika het hoë vlakke van genetiese diversiteit en dus hang die susksesvolle toepassing van Farmakogenetika in Suid-Afrika af van die voorlopige analise van die genetiese profiele van die Suid-Afrikaanse bevolkingsgroepe. Om hierdie rede was die doel van hierdie studie om die geneesmiddel metaboliseerings geen, CYP2C19, in ’n Suid-Afrikaanse Xhosa bevolkingsgroep te karakteriseer. Die CYP2C19 volgorde van 15 Xhosa individue is bepaal om die algemene variasie teenwoordig in die CYP2C19 geen te bevestig. Hierdie variasies is deur verskeie in silico analises geprioritiseer vir verder restriksie fragment lengte polimorfisme (RFLP) genotipering in 85 gesonde Xhosa individue om die frekwensie in ’n groter groep te bevestig, terwyl die kopie aantal variasie teenwoordig in hierdie 100 Xhosas geanaliseer is met Taqman® CNV toetse. Om die in silico data vir die 5’-stroomop variante funksioneel te bevestig, is daar gebruik gemaak van tweedeelige luciferase verklikker toetse. Verder is multi-spesie vergelykings gebruik om 5’-stroomop streke met hoë vlakke van ooreenstemming te identifiseer, terwyl CpG-eiland analise gebruik is om moontlike CpG-eilande in die omgewing van die CYP2C gene te identifiseer. Met behulp van volgorde bepaling van die CYP2C19 geen, is 30 variante geïdentifiseer. Uit hierdie variante was vyf vir die eerste keer met hierdie studie opgespoor. Met die gebruik van RFLP analise, is die alleel definerende variante naamlik CYP2C19*2, CYP2C19*9, CYP2C19*15 and CYP2C19*17, teen ’n frekwensie van 0.21, 0.09, 0.09 en 0.10 in die Xhosa bevolkingsgroep gevind. Verder was die nie-sinonieme variant, V374I, wat vir die eerst keer geïdentifiseer en CYP2C19*28 genoem is, teen ‘n frekwensie van 0.01 gevind. Tweedeelige luciferase verklikker toetse het bewys dat die konstruk met die rs7902257 variant ‘n beduidende afname in induksie in vergelyking met die “wilde tipe” konstruk gewys het (P = 0.0077). Hierdie variant was CYP2C19*27 genoem en was teen ’n frekwensie van 0.33 in die Xhosa bevolking gevind. Die multi-spesie vergelykings het vier gekonserveerde streke geïdentifiseer wat in LINE L1 herhalende elemente gevind is. Alhoewel CpG-eilande in die omgewing van die CYP2C gene gevind is, kon geen direkte korrelasies gemaak word tussen die veranderinge in uitdrukking van die gene en die teenwoordigheid van die CpG-eilande nie. Die rol van hierdie eilande met betrekking tot epigenetiese regulasie van hierdie gene moet dus nog ontrafel word. Tot ons kennis het hierdie projek die mees voledige inligting vir CYP2C19 in ’n Suid-Afrikaanse bevolkingsgroep gegee en het bewys dat die Xhosa bevolkingsgroep ‘n unieke genetiese profiel vertoon, wat van ander bevolkingsgroepe, insluitend die Kaapse Gemenge Herkoms populasie van Suid-Afrika, verskil het. Indien farmokogenetika suksesvol in die diverse bevolkingsgroepe van Suid-Afrika toegepas kan word, moet daar gebruik gemaak word van nuwe genotipering metodes.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-03-06T14:02:56Z No. of bitstreams: 2 Dissertação - Agostinho Tavares Semedo - 2017.pdf: 2917656 bytes, checksum: 0a4e0b9aac67ef54832262a3818baf13 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-03-06T14:03:17Z (GMT) No. of bitstreams: 2 Dissertação - Agostinho Tavares Semedo - 2017.pdf: 2917656 bytes, checksum: 0a4e0b9aac67ef54832262a3818baf13 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-03-06T14:03:17Z (GMT). No. of bitstreams: 2 Dissertação - Agostinho Tavares Semedo - 2017.pdf: 2917656 bytes, checksum: 0a4e0b9aac67ef54832262a3818baf13 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-02-22 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Clozapine (CLZ) has been an antipsychotic of choice in treatment refractory schizophrenia (TRS). However, around 30% of the patients do not respond appropriately to this antipsychotic, being in this way, super-refractory schizophrenia (SRS). Genetic polymorphisms from cytochrome P450 enzymes can influence the metabolism of drugs and individual variability therapeutic response. Considering CYP2C19 a polymorphic enzyme with second major participation in the metabolism of CLZ, the aim of the present study was to analyse the influence of CYP2C19*2 and *17 polymorphisms in the response to the treatment to CLZ. The present study included 69 schizophrenic patients and 137 healthy individuals as a control group. Genotyping test and analysis of polymorphisms was done using sequencing technique and enzymatic restriction (RFLP) for patients and control’s group respectively. The results showed a major distribution of CYP2C19*17 polymorphism in patients’s group in comparison to control’s group. The CYP2C19*2 polymorphism was significantly higher in patients with TRS than to patients with SRS. The CYP2C19*17 polymorphism in heterozygous (CYP2C19*1/*17) was associated to higher clozapine’s doses in polytherapy and less efficient therapeutic response in SRS patients’s group, while the CYP2C19*2 was associated to lower clozapine’s doses in monotherapy and good therapeutic response in TRS patients’s group. In addition, parameters like daily mean clozapine dose, symptons severity according to Brief Psyquiatric Rating Scale (BPRS) and female individuals were also associated to super-refractoriness response to CLZ having a major distribution in SRS patients’s group. These findings suggest that new treatment strategies must be evaluated for the patients carriers of CYP2C19*17 polymorphism with SRS, above all the female individuals. Future studies with larger sample should be relevant to give more consistence to these findings. / A clozapina (CLZ) é um antipsicótico de escolha no tratamento de esquizofrenia refratária (ER). No entanto, cerca de 30% dos pacientes não respondem adequadamente à este antipsicótico, sendo considerados super-refratários ao tratamento (ESR). Sabe-se que polimorfismos genéticos nas enzimas do citocromo P450 podem influenciar o metabolismo das drogas, interferindo na variabilidade individual de resposta terapêutica. Sendo a CYP2C19 uma enzima altamente polimórfica e com a segunda maior participação no metabolismo da CLZ, o presente estudo visou analisar as influências dos polimorfismos CYP2C19*2 e *17 na resposta ao tratamento à este antipsicótico. O estudo incluiu 69 pacientes diagnosticados com esquizofrenia e 137 indivíduos saudáveis como controle. Utilizou-se a técnica de sequenciamento na genotipagem dos pacientes e a restrição enzimática (RFLP- Restrition Fragment Length Polymorphism) para o controle. Os resultados mostraram uma maior distribuição do polimorfismo CYP2C19*17 no grupo dos pacientes em comparação ao grupo controle. O polimorfismo CYP2C19*2 teve uma maior distribuição no grupo dos pacientes com ER em comparação aos pacientes com ESR. O polimorfismo CYP2C19*17 em heterozigose (CYP2C19*1/*17) estava associado à maior dose de CLZ em politerapia e resposta terapêutica menos eficiente no grupo dos pacientes com ESR, enquanto que a CYP2C19*2 em heterozigose estava associado à menor dose de CLZ em monoterapia e à boa resposta terapêutica nos pacientes com ER. Notou-se também uma associação da média da dose diária de CLZ, da gravidade sintomatológica (BPRS) e dos indivíduos do sexo feminino à super-refratariedade de resposta ao tratamento à clozapina tendo esses parâmetros uma maior distribuição no grupo dos pacientes com esquizofrenia super-refratária. Esses achados sugerem que outras estratégias de tratamento sejam avaliadas para os pacientes portadores do polimorfismo CYP2C19*17 diagnosticados com ESR, sobretudo os do sexo feminino. Futuros estudos com amostras mais alargadas seriam relevantes para dar uma maior consistência a esses achados.

No description available.

Thesis (Ph.D.)--University of Alabama at Birmingham, 2009. / Title from PDF title page (viewed on Sept. 9, 2009). Includes bibliographical references.

Mehrere Studien wiesen eine Beteiligung der Enzyme CYP2D6, CYP2C19 und CYP2C9 am Metabolismus von trizyklischen Antidepressiva nach. Wir untersuchten die Auswirkungen genetischer Polymorphismen dieser Enzyme auf die Pharmakokinetik von E-, Z-Doxepin und Trimipramin beim Menschen. Eine einzelne orale Dosis von jeweils 75 mg Trimipramin und Doxepin wurde 42 gesunden Probanden verabreicht, die als Schnell- (EM), Intermediär- (IM) und Langsammetabolisierer (PM) von CYP2D6- und CYP2C19-Substraten und als Langsammetabolisierer mit dem CYP2C9-Genotyp *3/*3 genotypisiert worden waren. Die Substrate sowie ihre aktiven Metaboliten wurden mittels HPLC im Plasma gemessen, Daten wurden mit nonparametrischen pharmakokinetischen Methoden analysiert und statistisch ausgewertet. Die mittlere E-Doxepin-Clearance (95%-KI) betrug 406 (390-445), 247 (241-271) and 127 (124-139) l/h bei CYP2D6-EMs, -IMs und –PMs und war auch bei Trägern des CYP2C9*3/*3-Genotyps signifikant niedriger (238 l/h). CYP2C19 beeinflusste die orale Clearance von Z-Doxepin um das 2,5-fache (73 l/h in CYP2C19-PMs verglichen mit 191 l/h bei EMs). Die AUC (0-48h) des aktiven Metaboliten Desmethyldoxepin war vom CYP2D6-Genotyp abhängig mit einem Median von 5,28, 1,35 und 1,28 nmol/l*h bei CYP2D6-PMs, -IMs und –EMs. Die mittlere orale Trimipramin-Clearance betrug 276 l/h (180-444) in der Referenzgruppe aber nur 36 l/h (24-48) bei CYP2D6-PMs. Die AUC von Desmethyltrimipramin war 40-fach höher bei CYP2D6-PMs als bei EMs (1,7 verglichen mit 0,04 mg/l*h bei EMs), aber unter der Nachweisgrenze bei den meisten Probanden mit CYP2C19- oder CYP2C9-Defizienz. Der CYP2D6-Polymorphismus wies eine starke Auswirkung auf die Pharmakokinetik von E-Doxepin und Trimipramin sowie eine ausgeprägte Stereoselektivität bei der Biotransformation von Doxepin auf. CYP2D6-PMs sind möglicherweise einem erhöhten Risiko für unerwünschte Nebenwirkungen ausgesetzt bei der Behandlung mit den EMpfohlenen Dosen dieser Antidepressiva. / Several studies have demonstrated involvement of the enzymes CYP2D6, CYP2C19 and CYP2C9 in the metabolism of tricyclic antidepressants. We studied the effects of genetic polymorphisms in these enzymes on E-,Z-doxepin and trimipramine pharmacokinetics in humans. A single orale dose of each 75 mg timipramine and doxepin was given to 42 healthy volunteers genotyped as extensive (EM), intermediate (IM) and poor (PM) metabolizers of substrates of CYP2D6 and of CYP2C19 and as slow metabolizers with the CYP2C9 genotype *3/*3. E-,Z-doxepin and -desmethyldoxepin as well as trimipramine and desmethyltrimipramine were quantified in plasma by HPLC. Data were analyzed by non-parametric pharmacokinetics and statistics. Mean E-doxepin clearance (95% confidence interval) was 406 (390-445), 247 (241-271) and 127 (124-139) l/h in EMs, IMs and PMs of CYP2D6 and was also significantly lower in carriers of CYP2C9*3/*3 (238 l/h). CYP2C19 was involved in Z-doxepin metabolism with 2.5-fold differences in oral clearances (73 l/h in CYP2C19 PMs compared with 191 l/h in EMs). The AUC (0-48 h) of the active metabolite desmethyldoxepin was dependent on CYP2D6 genotype with a median of 5.28, 1.35 and 1.28 nmol/l*h in PMs, IMs and EMs of CYP2D6. The genetically polymorphic enzymes exhibited highly stereoselective effects on doxepin biotransformation in humans. The median oral clearance of trimipramine was 276 l/h (180-444) in the reference group but only 36 l/h (24-48) in CYP2D6-PMs. The AUC of desmethyltrimipramine was 40-fold greater in CYP2D6 PMs than in the reference group (1.7 vs. 0.04 mg/l*h in EMs), but below the quantification limit in most carriers of deficiencies of CYP2C19 or CYP2C9. The CYP2D6 polymorphism had a strong impact on E-doxepin and trimipramine pharmacokinetics and CYP2D6-PMs might be at an elevated risk for adverse drug effects when treated with common recommended doses of these antidepressants.

Im Bereich der medikamentösen antidepressiven Therapie ist die Bedeutung von erblichen Polymorphismen arzneistoffmetabolisierender Enzyme bereits in vielen Studien untersucht und gezeigt worden. Die meisten Antidepressiva werden über polymorphe Cytochrom-P450-Enzyme verstoffwechselt. Diese Arbeit befasst sich mit der Fragestellung, ob die Häufigkeitsverteilung der CYP2D6-, CYP2C19- und CYP2C9-Allele in der an Depression erkrankten Studienpopulation sich von der in der Normalbevölkerung unterscheidet und ob Veränderungen in der Pharmakokinetik, wie sie durch Cytochrom-P450-Polymorphismen verursacht werden, unter normalen klinischen Bedingungen Auswirkungen auf die Wirksamkeit der antidepressiven Therapie, die Nebenwirkungsrate und den Verlauf der Erkrankung haben. Im Rahmen dieser Arbeit wurden 334 Patienten auf die häufigsten CYP2D6-Allele (*3,*4,*5,*6 und Duplikation) und CYP2C19- und CYP2C9-Allele *2 und *3 mittels Genotypisierung untersucht. Die Bestimmung der seltener auftretender CYP2D6-Allele (*8,*9,*10,*17,*2 und *41) erfolgte zusätzlich bei 200 Patienten. Die entsprechenden klinischen Fragebögen mit Angaben zur Anamnese, Schwere der Erkrankung, Therapieverlauf und Nebenwirkungsprofil wurden von 233 Patienten in Abhängigkeit des CYP2D6- und CYP2C19-Genotyps ausgewertet. Für die Beurteilung des Langzeittherapieverlaufs standen jedoch deutlich weniger Patientendaten zur Verfügung, so dass die Ergebnisse zum Teil nur für den CYPD6-Genotyp ausgewertet werden konnten. Die genetischen Analysen ergaben, dass die Häufigkeitsverteilung der CYP2D6-, CYP2C19- und CYP2C9-Polymorphismen in der untersuchten Studienpopulation keine signifikante Änderung im Vergleich zur Normalbevölkerung aufwies. Während der Einfluss der CYP2D6-Genotypen auf pharmakokinetische Parameter eindeutig nachgewiesen ist, konnten die Ergebnisse dieser Arbeit weitestgehend keinen Zusammenhang zwischen der Schwere der Depression, der Therapieresponse, der Häufigkeit und Schwere der Nebenwirkungen und dem CYP2D6- und CYP2C19-Genotyp herstellen. / The importance of genetic polymorphisms of drug metablizing enzymes have been already investigated und proved in many studies before. Most of antidepressants are metabolized by cytochrome P450 enzymes. The aim of this study was to determine if there is a difference in the distribution of CYP2D6-, CYP2C19- and CYP2C9-allels in inpatients with major depression in comparison to the healthy population and if changes in the pharmacokinatic, created by cytochrome P450 polymorphisms, can be have effects on the efficacy of antidepressant therapy, rate of intolerable side effects and development of the depression. We examined 334 patients by genotyping for the most important CYP2D6-allels (*3,*4,*6,*5 und duplication) and the CYP2C19- and CYP2C9-allels *2 and *3. Further 200 patients were tested for the more infrequent CYP2D6-allels (*8,*9,*10,*17,*2 and *41). The corresponding clinical questionnaires containing informations about the anamnesis, severity of the desease, therapeutic outcome and intolerable side effects have been evaluated of 233 patients in dependence of the CYP2D6- and CYP2C19-genotype. There were significant less clinical datas for the evaluation of long term therapy response be available, so that the results could be partially only analysed for the CYP2D6-genotype. The genetic analysis detected that the distribution of the CYP2D6-, CYP2C19- and CYP2C9-polymorphismen in the study population didn´t reached significant changes in comparison to the healthy population. While the influence of CYP2D6-genotypes on pharmacokinatic parameters is clear demonstrated, the results of this study mainly couldn´t establish a relation between the severity of depression, therapeutic response, frequency and severity of side effects and the CYP2D6 and CYP2C19-genotype.

No description available.

The Cytochrome P450 family of enzymes is responsible for the majority of Phase I metabolism, and has been identified as an important source of pharmacokinetic variation in therapeutic responses. CYP2C19 and CYP2D6, metabolising >35% of commonly prescribed medications, are two of the most important pharmacogenetic markers that have been studied with the aim of improving treatment response and reducing adverse drug reactions. The Food and Drug Administration (FDA) approved AmpliChip CYP450 Test (AmpliChip) was compared to a previously developed PCR-RFLP platform and a newly developed XLPCR+ Sequencing platform for the ability to identifying genotype and predicting phenotype for CYP2C19 and CYP2D6 respectively. The AmpliChip was found not to be genotypically comprehensive enough for evaluating CYP2C19 genotype, not robust enough for determining CYP2D6 genotype and inaccurate in predicting phenotype for both. The XLPCR+ Sequencing method identified three novel alleles and one sub-variant. Advances in online column-switching solid phase extraction generated a rapid and robust LCMS/ MS method for simultaneously quantifying the probe drugs omeprazole (CYP2C19 substrate), dextromethorphan (CYP2D6 substrate) and their metabolites. Antimodes were identified for phenotypic cut-offs which offered measured phenotype for comparison to predicted phenotype. Omeprazole metabolism by CYP2C19 correlated well with predicted phenotype in a demographically representative South African cohort. There are concerns regarding the use of omeprazole as a probe drug as participants predicted to be ultrarapid metabolisers for CYP2C19 had similar rates to extensive metabolisers. Regardless of this concern, decreased metabolism was assigned to the CYP2C19*15 for the first time. CYP2D6 predicted phenotype correlated very well with measured phenotype, validating the suitability of dextromethorphan use for measuring CYP2D6 metabolism. Substrate modified activity score using 0.5 to predict intermediate metabolisers fine-tuned the XLPCR+ Sequencing platform for phenotype prediction. This finding, along with observations in CYP2C19 metabolism of omeprazole, highlights the importance of substrate specific phenotype prediction strategies. Controversially, attempts to associate CYP2D6 phenotype prediction with risperidone-related adverse drug reactions has yielded conflicting results. The XL-PCR+Sequencing platform was able to discount this association by predicting a variety of metabolisers in a pilot cohort selected to be experiencing risperidone-related adverse drug reactions. The comprehensive capability of the XL-PCR+Sequencing allowed for the identification of an additional novel allele in this cohort. The data presented in thisthesis has provided insight into the relationship between predicted and measured phenotype for CYP2C19 and CYP2D6 in the South African population. The XL-PCR+Sequencing platform can be used for future research or can be applied to improve treatment outcome. The LC-MS/MS method developed could be used for future evaluations of predicted and measured phenotype with the ability to be adjusted for therapeutic drug monitoring. This thesis advances pharmacogenetics of CYP2C19 and CYP2D6 for use in the South African population. / Thesis (PhD)--University of Pretoria, 2013. / gm2014 / Pharmacology / unrestricted

No description available.

55 Abstract Frequency of selected genetic polymorphisms of cytochrome P450 in the Czech population and the influence of CYP2C9 genotype on the hypolipidemic effect of fluvastatin Introduction: One of the main factors of genetically determined variability in response of humans to administered drugs are differences in catalytic activity of metabolizing enzymes, which are caused mainly by genetic polymorphisms in cytochrom P450 family enzymes. This thesis consists of two parts and it is presented as a commentary to the original papers. The first aim was to investigate the frequency of functionally important variant alleles of three main isoenzymes of cytochrome P450 gene: CYP2D6, CYP2C9, CYP2C19, throughout the Czech population, predict the prevalence of poor metabolizer phenotypes, and then to compare the results to the data from other populations. Secondly, we analysed the correlation between the CYP2C9 genotype and cholesterol-lowering effect of fluvastatin in human hypercholesterolemic patients. Methods: Genotypes were determined by PCR-RFLP. The presence of alleles CYP2D6*1, *6, *5, *4, *3, and gene duplication was analysed in 233 healthy volunteers, CYP2C9*1, *2 and*3 in 254 subjects and CYP2C19*1, *2 and *2 in 218 subjects. Eighty seven patients on fluvastatin therapy, and 48 patients on monotherapy...